Obesity Data Analysis

3.1 Summary of findings

In the next few subsections, we dive into the details of how we drew these conclusions.

3.2 Data pre-processing

To conduct deeper analysis on our data, we added the following columns to our dataset:

BMI: the Body Mass Index of each person, a continuous variable calculated using the World Health Organization guideline: \(BMI = \frac{Weight}{Height^2}\).
IsOverweight: a binary categorical value whose value is 1 if the BMI of the person is more than 25, 0 otherwise.

These columns serve as alternate metrics of the obesity of an individual, a continuous variable and a binary categorical variable, to complement NObeyesdad, the obesity category level which is a ordinal categorical variable.

These new columns can be found and used directly in the dataset scripts/xinyi-zhao_files/CleanObesityDataSet.csv.

In order to improve the visualization of certain plots, we also made local modifications to the data types of some columns for only that given plot. For instance, to plot the alluvial diagrams (figure 10), we rounded the values of the following: Frequency of consumption of vegetables (FCVC), Number of main meals (NCP), Physical activity frequency (FAF), Time using technology devices (TUE) (some of the values of these variables were floats, presumably because the researchers took an average of multiple time periods). This made sure that the variables are discrete (whole numbers).

3.3 Analysis of Height, Weight and BMI variables

Since the dataset contains artificially generated data, we first needed to verify that the dataset matches our expectations, notably by visualizing the distribution of these three continuous variables.

Importing the necessary libraries and dataset

Code

library(readr)
library(dplyr)
library(tidyverse)
library(stats)
library(vcd)
library(ggplot2)
library(gridExtra)
library(grid)
library(GGally)
library(reshape2)
library(colorspace)
library(plyr)
library(ggalluvial) 
library(ggridges)

data <- read_csv('scripts/xinyi-zhao_files/CleanObesityDataSet.csv',show_col_types = FALSE)

Preliminary verifications of the number of rows, columns and missing values of our dataset show that there does not seem to be any problems with the structure of our dataset.

Code

cat("Number of rows in dataset: ", nrow(data), "\nNumber of columns in dataset: ", ncol(data),"\nNumber of missing values in dataset: ", sum(is.na(data)))

Number of rows in dataset:  2111 
Number of columns in dataset:  20 
Number of missing values in dataset:  0

Additionally, the data seems to align with our expectations, visualizing the Height, Weight and BMI variables shows that there are no biases with respect to the people surveyed.

Code

# Histograms of Height, Weight and BMI

plot1 <- ggplot(data = data, aes(x = Height)) + geom_histogram(binwidth = 0.02)
plot2 <- ggplot(data = data, aes(x = Weight)) + geom_histogram(binwidth = 2)
plot3 <- ggplot(data = data, aes(x = BMI)) + geom_histogram(binwidth = 1)
grid.arrange(plot1, plot2, plot3, ncol = 3,
     top = textGrob("Histograms of the continuous variables Height, Weight and BMI",gp=gpar(fontsize=16)))

Fig. 1: Histograms of Height, Weight and BMI

Code

shapiro.test(data$Height)


    Shapiro-Wilk normality test

data:  data$Height
W = 0.99323, p-value = 2.772e-08

Code

shapiro.test(data$Weight)


    Shapiro-Wilk normality test

data:  data$Weight
W = 0.9765, p-value < 2.2e-16

Code

shapiro.test(data$BMI)


    Shapiro-Wilk normality test

data:  data$BMI
W = 0.97475, p-value < 2.2e-16

Code

plot1 <- ggplot(data, aes(sample = Height)) + 
  stat_qq() + 
  stat_qq_line(col = "navy") +
  xlab("Height")

plot2 <- ggplot(data, aes(sample = Weight)) + 
  stat_qq() + 
  stat_qq_line(col = "navy") +
  xlab("Weight")

plot3 <- ggplot(data, aes(sample = BMI)) + 
  stat_qq() + 
  stat_qq_line(col = "navy") +
  xlab("BMI")

grid.arrange(plot1, plot2, plot3, ncol = 3)

Fig. 2: QQ-Plot of Height, Weight and BMI

Analysis:

On the histogram, it is not possible to tell for all three continuous variables whether they follow a normal

The height of the individuals appears to follow a normal distribution, which is aligned with our expectations as it is an assumption that researchers typically make.
The weight of the individuals does not appear to be normally distribution as it has a right skew. Body weight is found to have a right skew according to research.
The BMI of individuals

Lastly, we plotted a boxplot to better understand the other statistics (e.g. median, outliers) of the variable BMI.

Code

# Boxplot to visualize the BMI across all individuals 
ggplot(data, aes(x=BMI)) + 
  geom_boxplot(fill = "lightblue", color = "black") + 
  coord_cartesian(ylim = c(-2, 2)) +  
  labs(title = "Boxplot of BMI across all individuals")

Fig. 3: Boxplot to visualize the BMI across all individuals

Code

fivenum(data$BMI)

[1] 12.99868 24.32580 28.71909 36.01650 50.81175

Code

ggplot(data, aes(x = Weight, y = NObeyesdad, fill = NObeyesdad)) +
  stat_density_ridges(alpha = 0.7) +
  scale_fill_viridis_d() +
  labs(title = "Ridgeline Plot of Obesity Types", x = "weight", y = "Obesity Type") +
  theme_ridges()

Fig. 4: Ridgeline Plot of weight of individuals across Obesity Types

3.4 Preliminary visualizations

Code

set.seed(123456)

data <- data %>%
 mutate_if(is.numeric, scale)

data_num <- data[c("Age", "Height", "Weight", "NCP", "CH2O", "FAF", "TUE","BMI")]

# Convert all columns to numeric
data_num <- sapply(data_num, as.numeric)

# Sample 1000 points for clearer visualization
data_sampled <- sample_n(as.data.frame(data_num), 300)

ggpairs(as.data.frame(data_sampled), aes(alpha = 0.4, size = 0.02), 
           upper = list(continuous = wrap("cor", size = 12))) + 
  theme(text = element_text(size = 35))

Fig. 5: Scatterplot of each pair of numeric variables in the dataset

Code

categories <- c('Insufficient_Weight','Normal_Weight', 'Overweight_Level_I', 'Overweight_Level_II', 'Obesity_Type_I', 'Obesity_Type_II','Obesity_Type_III')

# Create a mapping from category to integer
category_mapping <- setNames(1:length(categories), categories)

data$NObesity_numeric <- as.integer(factor(data$NObeyesdad, levels = categories))

data_pca <- data[c("FCVC","NCP","FAF","TUE","NObesity_numeric")]


cor_matrix <- cor(data_pca)

# Reshape the data for heatmap
melted_cor <- melt(cor_matrix)

# Creating heatmap
ggplot(melted_cor, aes(Var1, Var2, fill = value)) +
  geom_tile() +
  geom_text(aes(label = ifelse(value > 0.1&value<1, round(value, 2), '')), color= 'darkblue',vjust = 1) +
  scale_fill_gradient2(midpoint = 0) +
  theme_minimal() +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  ggtitle("Heatmap of Correlations")

Fig. 6: Heatmap of correlations between numerical variables

Code

# Creating individual density plots with smooth lines
plot_fcvc <- ggplot(data, aes(x = FCVC)) + 
  stat_density(aes(y = ..density..), geom = "area", fill="blue", alpha=0.5) +
  ggtitle("FCVC Density Plot") +
  xlab("FCVC") +
  ylab("Density")

plot_ncp <- ggplot(data, aes(x = NCP)) + 
  stat_density(aes(y = ..density..), geom = "area", fill="blue", alpha=0.5) +
  ggtitle("NCP Density Plot") +
  xlab("NCP") +
  ylab("Density")

plot_faf <- ggplot(data, aes(x = FAF)) + 
  stat_density(aes(y = ..density..), geom = "area", fill="blue", alpha=0.5) +
  ggtitle("FAF Density Plot") +
  xlab("FAF") +
  ylab("Density")

plot_tue <- ggplot(data, aes(x = TUE)) + 
  stat_density(aes(y = ..density..), geom = "area", fill="blue", alpha=0.5) +ggtitle("TUE Density Plot") +
  xlab("TUE") +
  ylab("Density")

# Arrange the plots in a 2x2 grid
grid.arrange(plot_fcvc, plot_ncp, plot_faf, plot_tue, nrow = 2)

Fig. 7: Density plots for Frequency of consumption of vegetables (FCVC), Number of main meals (NCP), Physical activity frequency (FAF), Time using technology devices (TUE)

3.5 Understanding the correlation between biological factors and obesity

3.6 Correlation between lifestyle habits and obesity

Code

# Create a mosaic plot for each variable in the table plotted against 'IsOverweight'

data_mosaic <- data[c("Gender", "family_history_with_overweight","FAVC","SMOKE","SCC","IsOverweight")]

data_mosaic$family_history_with_overweight <- fct_relevel(data_mosaic$family_history_with_overweight, "yes", "no")

data_mosaic$SMOKE <- fct_relevel(data_mosaic$SMOKE, "yes", "no")

data_mosaic$FAVC <- fct_relevel(data_mosaic$FAVC, "yes", "no")

data_mosaic$SCC <- fct_relevel(data_mosaic$SCC, "yes", "no")


data_mosaic$IsOverweight <- as.character(data_mosaic$IsOverweight)

for(var in names(data_mosaic)[names(data_mosaic) != "IsOverweight"]) {
# png(paste0("mosaic_", var, "_IsOverweight.png"))
 contingency_table <- table(data_mosaic[[var]],data_mosaic$IsOverweight)
 mosaicplot(contingency_table, main = paste("Mosaic Plot for", var), ylab = "Is Overweight", xlab = var, col = c("pink", "brown"))
# dev.off()
}

Fig. 8a: Mosaic Plot of Gender against IsOverweight

Fig. 8b: Mosaic Plot of Family History against IsOverweight

Fig. 8c: Mosaic Plot of Frequent consumption of high caloric food against IsOverweight

Fig. 8d: Mosaic Plot of weight of whether the person smokes against IsOverweight

Fig. 8e: Mosaic Plot of calories consumption monitoring against IsOverweight

Code

# plot 1 mosaic 3 var
library(colorspace)
library(plyr)

data_mosaic <- data[c("FAVC", "SCC", "IsOverweight")] 
data_mosaic <- dplyr::count_(data_mosaic,vars = c("FAVC", "SCC", "IsOverweight"))

colnames(data_mosaic)[colnames(data_mosaic) == "n"] <- "Freq"

data_mosaic$IsOverweight <- fct_rev(as.character(data_mosaic$IsOverweight))

mosaic(FAVC ~ SCC + IsOverweight, data = data_mosaic, direction = c("v","h","v"), highlighting_fill = c("#bdd7e7","#2171b5"))

Fig. 9: Trivariate mosaic plot visualizing frequent consumption of high caloric food, calories consumption monitoring and IsOverweight

Code

data_alluvial <- data[c("Age", "NObeyesdad", "NCP", "CH2O", "FAF", "CALC", "TUE")]

data_alluvial$CH2O <- as.numeric(data_alluvial$CH2O)
data_alluvial$CH2O <- round(data_alluvial$CH2O)
data_alluvial$NCP <- as.numeric(data_alluvial$NCP)
data_alluvial$NCP <- round(data_alluvial$NCP)
data_alluvial$FAF <- as.numeric(data_alluvial$FAF)
data_alluvial$FAF <- round(data_alluvial$FAF)
data_alluvial$TUE <- as.numeric(data_alluvial$TUE)
data_alluvial$TUE <- round(data_alluvial$TUE)

data_alluvial <- data_alluvial %>%
 mutate(Obesity_Category = case_when(
   NObeyesdad %in% c("Overweight_Level_I", "Overweight_Level_II") ~ "Overweight",
   NObeyesdad %in% c("Obesity_Type_I", "Obesity_Type_II") ~ "Obese",
   NObeyesdad == "Normal_Weight" ~ "Normal",
   NObeyesdad == "Insufficient_Weight" ~ "Underweight"
 ))

Code

data_alluvial_2 <- dplyr::count_(data_alluvial,vars = c("Obesity_Category", "FAF", "CALC", "NCP", "CH2O", "TUE"))

colnames(data_alluvial_2)[colnames(data_alluvial_2) == "n"] <- "Freq"

data_alluvial_2$Obesity_Category <- factor(data_alluvial_2$Obesity_Category, levels = c("Underweight", "Normal", "Overweight", "Obese"))

ggplot(as.data.frame(data_alluvial_2), aes(y = Freq, axis1 = Obesity_Category, axis2 = TUE, axis3 = FAF)) +
  geom_alluvium(aes(fill = Obesity_Category), width = 1/12) +
  geom_stratum(width = 1/12, fill = "grey80", color = "grey") +
  geom_label(stat = "stratum", aes(label = after_stat(stratum))) +
  scale_x_discrete(limits = c("Gender", "Dept"), expand = c(.05, .05)) +
  scale_fill_brewer(type = "qual", palette = "Set1")  + 
  expand_limits(x = 0, y = 0) +
  ggtitle("Obesity category vs Time on Electronics vs Alcohol consumption") + 
  theme_void() +
  theme(plot.margin = margin(0,0,0,0, "cm"))

Fig. 10a: Alluvial diagram of Obesity category vs Time on Electronics vs Alcohol consumption

Code

# CALC (consumption of alcohol), TUE (time on electronics), FAF (physical activity), CH2O (daily water), NCP (number of main meals)
ggplot(as.data.frame(data_alluvial_2), aes(y = Freq, axis1 = Obesity_Category, axis2 = NCP, axis3 = CH2O)) +
  geom_alluvium(aes(fill = Obesity_Category), width = 1/12) +
  geom_stratum(width = 1/12, fill = "grey80", color = "grey") +
  geom_label(stat = "stratum", aes(label = after_stat(stratum))) +
  scale_x_discrete(limits = c("Gender", "Dept"), expand = c(.05, .05)) +
  scale_fill_brewer(type = "qual", palette = "Set1")  + 
  expand_limits(x = 0, y = 0) +
  ggtitle("Obesity category vs Nb of meals vs Water consumption a day") + 
  theme_void() +
  theme(plot.margin = margin(0,0,0,0, "cm"))

Fig. 10b: Alluvial diagram of Obesity category vs Nb of meals vs Water consumption a day